If you only count time in the air, a flight always beats a train. But almost no one travels purely "in the air". Between getting to the airport, security, boarding, taxiing, baggage and the trip back into the destination city, a typical short-haul flight has 2 to 3 hours of overhead before its scheduled 1-2 hours of actual flight time. A high-speed train starts and ends in city centres, with 10 minutes of boarding instead of 90.
That's where the tipping point comes from. On routes under about 600 km — Paris–London, Rome–Florence, Madrid–Barcelona, Berlin–Hamburg — the train usually beats the flight door-to-door even before you factor in price. On routes 600 to 1,000 km it depends: a high-speed corridor like Paris–Marseille or Frankfurt–Berlin still beats flying once you count overhead, but a slow cross-border route may not.
Cost follows similar geometry. Trains charge for distance plus a corridor premium; flights have a fixed cost floor (airport fees, fuel for takeoff, ground crew) that low-cost carriers compensate for with extras. A typical Madrid–Barcelona ticket on AVE booked two weeks ahead beats a Ryanair Madrid–Barcelona ticket once you add baggage and seat fees. London–Edinburgh by LNER beats a London–Edinburgh flight once you add the £25 each way to and from Stansted.
The big argument is climate. Per passenger-kilometre, a typical European electric train emits around 14 grams of CO₂. A short-haul flight: about 156. That's an order of magnitude. On a 1,000 km route, you're choosing between roughly 14 kg of CO₂ by train and roughly 156 kg by air. For most travellers, that's the most consequential choice they make all year.
Where flying still wins: anything that crosses open water without a tunnel (Reykjavik to anywhere, Dublin to most of the continent, Malta to anywhere). Anything over 1,500 km where a single train day becomes two with an overnight stop. And anything where you genuinely don't have a day to spare and the flight beats train despite all the overhead.
Pick your route from the city list and compare both options yourself. The math will surprise you on at least one corridor you assumed had to be a flight.